From: Xander Gonzalez (xandergonz1_at_gmail.com)
Date: Wed Jul 10 2019 - 13:18:33 CDT
---------- Forwarded message ---------
From: Xander Gonzalez <xandergonz1_at_gmail.com>
Date: Tue, Jul 9, 2019 at 3:54 PM
Subject: Re: namd-l: Colvars Orientation Question
To: Jérôme Hénin <jerome.henin_at_ibpc.fr>
Thank you again for your advice, I did this and am receiving large values
for the energy, around 10^4. I am also receiving large values for the force
quaternions, around 10^4 again. Do you have any further advice for
continuing?
Regards,
Alexander
On Tue, Jul 9, 2019 at 4:49 AM Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
> Hi Alexander,
>
> To get a full view of the process, you can enable outputEnergy for the
> harmonic bias and outputAppliedForce for the collective variables. If the
> deviations are large you should see high energies and forces.
>
> Best,
> Jerome
>
>
>
> On Fri, 5 Jul 2019 at 21:23, Xander Gonzalez <xandergonz1_at_gmail.com>
> wrote:
>
>> Thank you for the response. I have checked the colvars.traj file and the
>> beginning quaternions are significantly different than the center colvars
>> set in the configuration file, and the final quaternions are different than
>> the target centers. I also visualized the rotations with the script you
>> sent, it seems like the initial rotation is caused by the second collective
>> variable rotating about 90 degrees. I have tried setting the target center
>> for the second colvar quaternion to be the same as it's center to see if
>> this would keep this rotation from happening, but I get the same result.
>>
>> Best,
>> Alexander
>>
>> On Wed, Jul 3, 2019 at 3:54 AM Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
>>
>>> One last point: quaternions values are not very intuitive. If it helps,
>>> you can visualize them as a rotation axis and lines indicating the value of
>>> the angle. Load a trajectory in VMD, source this script and use the
>>> "start_rotation_display" command, with the name of the orientation colvar.
>>>
>>> https://github.com/Colvars/colvars/blob/master/vmd/scripts/colvar_display.tcl
>>>
>>> Best,
>>> Jerome
>>>
>>> On Wed, 3 Jul 2019 at 10:49, Jérôme Hénin <jerome.henin_at_ibpc.fr> wrote:
>>>
>>>> Hi Alexander,
>>>>
>>>> the explanation to this mystery might be in the colvars.traj file. Look
>>>> in particular for the initial and final values of the orientation
>>>> quaternion.
>>>>
>>>> Jerome
>>>>
>>>> On Tue, 2 Jul 2019 at 23:50, Xander Gonzalez <xandergonz1_at_gmail.com>
>>>> wrote:
>>>>
>>>>> Thank you for the feedback, I have been trying to run a static
>>>>> harmonic restraint and running into some trouble. I have tried setting
>>>>> targetCenters to the same as Centers as well as not using targetCenters at
>>>>> all. Both result in the protein making what seems to be a complete
>>>>> rotation. Setting forceConstant as 1 seems to result in a static protein,
>>>>> but I am not sure if this is correct. Did you have any specific ideas about
>>>>> how to create a static harmonic restraint? Or do the results that I have
>>>>> been getting imply something about the system?
>>>>>
>>>>> Thank you again,
>>>>> Alexander
>>>>>
>>>>> On Mon, Jul 1, 2019 at 7:02 PM Giacomo Fiorin <
>>>>> giacomo.fiorin_at_gmail.com> wrote:
>>>>>
>>>>>> Hi Alex, it is likely that the combined effect of the two rotations
>>>>>> that you are applying is inducing a torque on the entire protein. Can you
>>>>>> try first to see if a static harmonic restraint is stable for this choice
>>>>>> of variable before starting to move it?
>>>>>>
>>>>>> Giacomo
>>>>>>
>>>>>> On Mon, Jul 1, 2019 at 4:01 PM Alexander Gonzalez <
>>>>>> acgonzalez_at_uchicago.edu> wrote:
>>>>>>
>>>>>>> Hello,
>>>>>>>
>>>>>>> I've been trying to run a simulation on a new structure with
>>>>>>> orientation collective variables to separate two portions of a protein
>>>>>>> (resid 43-515 and resid 542-1011), I followed the "Exploring Complex
>>>>>>> Conformational Transition Pathways" tutorial, using the provided
>>>>>>> orientation.tcl to find the orientation quaternions. I changed the
>>>>>>> colvars.conf file as is shown below:
>>>>>>>
>>>>>>> #############################################################
>>>>>>> ## Collective Variables ##
>>>>>>> #############################################################
>>>>>>>
>>>>>>> # Global parameters
>>>>>>> colvarsTrajFrequency 500
>>>>>>>
>>>>>>> colvar {
>>>>>>> name d1_2
>>>>>>> orientation {
>>>>>>> atoms {
>>>>>>> psfSegID AP1
>>>>>>> atomNameResidueRange { CA 43-515 }
>>>>>>> }
>>>>>>> refPositionsFile
>>>>>>> CC-complete-model-ChainA-solvate-centered-mini-LF.pdb
>>>>>>> }
>>>>>>> }
>>>>>>>
>>>>>>> colvar {
>>>>>>> name d3_4
>>>>>>> orientation {
>>>>>>> atoms {
>>>>>>> psfSegID AP1
>>>>>>> atomNameResidueRange { CA 542-1011 }
>>>>>>> }
>>>>>>> refPositionsFile
>>>>>>> CC-complete-model-ChainA-solvate-centered-mini-LF.pdb
>>>>>>> }
>>>>>>> }
>>>>>>>
>>>>>>> harmonic {
>>>>>>> name harm
>>>>>>> colvars { d1_2 d3_4 }
>>>>>>> # initial values
>>>>>>> centers { ( 1 , 0 , 0 , 0 ) ( 1 , 0 , 0 , 0 ) }
>>>>>>> # target values
>>>>>>> targetCenters { ( 0.984807753012208 , -0.009832450473359431 ,
>>>>>>> 0.04197699686335437 , 0.16821101136975466 ) ( 0.984807753012208 ,
>>>>>>> 0.009832450473359431 , -0.04197699686335437 , -0.16821101136975466 ) }
>>>>>>> # force constant in kcal/(mol*rad^2)
>>>>>>> forceConstant 10000
>>>>>>> # steering protocol time
>>>>>>> targetNumSteps 200000
>>>>>>> # calculate work
>>>>>>> outputAccumulatedWork on
>>>>>>> }
>>>>>>>
>>>>>>> The resulting simulation seems to separate the two protein sections,
>>>>>>> but not before rotating and distorting the protein for the first few
>>>>>>> frames. I also tried accomplishing this separation with the spin colvars,
>>>>>>> where I used the axis.tcl script to get the principal axes. Drawing these
>>>>>>> axes seems to show that they are accurate for the rotation that I want to
>>>>>>> accomplish. Despite this, the spin colvar simulation also leads to the
>>>>>>> structure rotating and distorting in unwanted ways for the first few frames
>>>>>>> of the simulation before separating as expected. I would really appreciate
>>>>>>> advice for possible things to try regarding this, also let me know if you
>>>>>>> want more information about the specific structure/simulation I am
>>>>>>> attempting. Thanks for your time!
>>>>>>>
>>>>>>
>>>>>>
>>>>>> --
>>>>>> Giacomo Fiorin
>>>>>> Associate Professor of Research, Temple University, Philadelphia, PA
>>>>>> Research collaborator, National Institutes of Health, Bethesda, MD
>>>>>> http://goo.gl/Q3TBQU
>>>>>> https://github.com/giacomofiorin
>>>>>>
>>>>>
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